A Glitch in the Matrix: Avoiding this sort of thing, when it comes to virtual reality, is one of the few legitimate uses for the Out-of-Mind visual textures. (Others mostly including hiding gifts and playing really terrible practical jokes.)
A more commonly seen variant are “weavespiders”, small metallic fractal spiders (which everyone knows to ignore) used in virtual realms to collect trash, reassemble broken scenery, and otherwise do maintenance. While, obviously enough, this can simply be done programmatically without requiring any visual metaphor, reifying them like this is a simple way of avoiding the uncanny valley effect of changes “just happening” with no apparent in-world cause.
Deep-Immersion Gaming: Sort of an inevitable consequence when the standard gaming rig involves full-sensory virtual reality of such quality as to be indistinguishable from reality, except for necessary departures of awesome. Although most people put together more imaginative avatars than looks-just-like-themselves.
(Now, the real deep-immersion gaming comes when you add a gnostic overlay that makes you believe that you’re your character and suppresses the memory of having been you, for the serious authenticity devotees. Ultimate realism, with only a slight to moderate chance of mental trauma. Personality shifts not included.)
We Will Not Use Photoshop in the Future: Oh, we definitely will, and we will also virtually film as-real-as-life virtual reality, too, just to make life more fun. But to nod in the direction of what nobody ever seems to not add, there’s a reason why all security cameras, most lifelogs, and a lot of other devices that record video automatically geotag, device-certify and cryptosign everything, and this is it.
Similar precautions, of course, in this sophotechnological future are needed for reliable memory.
Mental Affair: Fairly common, or at least the “virtual reality” kind is; species generally don’t come equipped with the necessary hardware to do this sort of thing naturally. Popular for a variety of reasons, including obviating distance, permitting all kinds of things from, well, extra stamina to Power Perversion Potential that the material world has, ah, trouble with, and – for those having sex outside their species – making Boldly Coming work for couples who don’t share the same atmospheric composition, pressure, and temperature requirements, or have other similarly extreme physical incompatibilities.
Inside a Computer System: Well, yes, this is how virtuality works; the computers simulate the entire environment in full fidelity – which, I hasten to add, means even more when you have to come up with appropriate outputs for all possible sensory ranges of your polyspecific clientele – and then your sensory-link implants substitute this input at the sensory center of your brain. Old technology – safe, reliable, boring, been around for millennia.
Does not, I repeat, not move your consciousness anywhere – it remains in the gooey paste inside your skull, or whatever else you happen to think with. That’s what differentiates virtuality from uploading (which in any case requires quantum processors, which is by no means all of them), or voodoo – but see below.
Digisapiences, and other native digital sapients, don’t actually dwell in virtual spaces inside computers, I hasten to add. They’re programs; their senses aren’t like ours, and don’t need concepts like “space” and “shape” and even occasionally “time” to work. They inhabit the processors raw.
Finally, while it’s not technically within the meaning of this trope, most people are at least partially within computer systems at all times, mostly because – once you get into the habit – most people’s minds are too big to fit in their brains any more. Most people in advanced societies live their lives surrounded by an exoself, a sort of computational fog of data and software agents and thought-threads and daemons and suchlike doing auxiliary cognitive tasks, and since there’s only so much computational power you can cart around personally, a lot of them offload the less important parts of their current thinking to processors out there, somewhere, in the cloud. (A bit difficult, of course, when abroad – hence, the existence of, among other solutions, thinking-brain dogs.)
Holodeck Malfunction: Utterly averted, with the possible minor exception of someone using a virtual reality version of a basilisk hack on you, but that’s not a malfunction, that’s deliberately exposing you to something that would be equally bad for you if you perceived it through any other sensory channel. But, in essence, what sort of idiot engineering gives a VR simulator privileged-channel access to your brain?